<h1>
How to create and access genome groups
</h1>

Creating a genome group in your workspace allows you to create logical
groups of genomes for downstream comparative analysis. In this
example, you will create two genome groups. One genome group will
contain only Streptococcus aureus, and the second genome group will
contain all Streptococcus genomes except those from Streptococcus
aureus.
<p>

This example assumes familiarity with a few other commands in the CLI
to create the input file containing the genomes to be put in the new
genome group. You do not need to be familiar with these commands, just
the format of the input file. The format of the input file is simply a
list of genome ids, one per line with no other information in the
file.
<p>
<pre>
$ p3-all-genomes --in genome_name,aureus > Staphylococcus.aureus.genomes
$ p3-all-genomes --in genome_name,Staphylococcus > Staphylococcus.all.genomes
$ a_not_b Staphylococcus.all.genomes Staphylococcus.aureus.genomes > Staphylococcus.not.aureus.genomes

$ wc *.genomes
    9257   41089  399759 Staphylococcus.all.genomes
    8383   36955  356756 Staphylococcus.aureus.genomes
     876    4146   43099 Staphylococcus.not.aureus.genomes
   18516   82190  799614 total
</pre>
<p>
Let's take a quick look at a few entries in each file using the unix
head command. In this case, the first five lines of each file are
displayed. Notice that the header exists in two of the three files. It
is not in the file created with the a_not_b command because the header
appeared in both input files to the a_not_b command.
<p>
<pre>
$ head -n 5 *.genomes
==> Staphylococcus.all.genomes <==
genome.genome_id
904758.3
904731.3
904739.3
904750.3

==> Staphylococcus.aureus.genomes <==
genome.genome_id
904758.3
904731.3
904739.3
904750.3

==> Staphylococcus.not.aureus.genomes <==
1000590.6
1008454.3
1034809.4
1078083.3
1115805.3
</pre>

<p>

The input files to create genome groups are almost ready. The input to
p3-put-genome-group is a single column file with the only values being
genome ids. The header needs to be removed. We can easily do this with
an editor, or use the unix grep command with the -v option. For this
example, we will just edit the file with an editor and remove the
header.
<p>
The p3-put-genome-group takes the list of genome ids on standard
input. Using the unix cat command we can send the contents of our
newly created files of genome ids to the p3-put-genome-group command
with the following command.
<p>
<pre>
$ cat Staphylococcus.not.aureus.genomes | p3-put-genome-group "Staphlococcus not aureus"
$ cat Staphylococcus.aureus.genomes | p3-put-genome-group "Staphylococcus aureus"
</pre>
<p>

The two newly created genome groups are now visible and usable in your
workspace using on the PATRIC web site, as well as accessible using
the command line interface.

<pre>
$ p3-get-genome-group "Staphylococcus aureus"
904758.3
904731.3
904739.3
904750.3
904763.3
904725.3
904734.3
904737.3
904754.3
904768.3
&lt;...>
</pre>

